Global promoter methylation analysis reveals novel candidate tumor suppressor genes in natural killer cell lymphoma

Can Küçük, Xiaozhou Hu, Bei Jiang, David L Klinkebiel, Huimin Geng, Qiang Gong, Alyssa Bouska, Javeed Iqbal, Philippe Gaulard, Timothy W. McKeithan, Wing C. Chan

Research output: Contribution to journalArticle

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Abstract

Purpose: To identify tumor suppressor genes epigenetically silenced by promoter hypermethylation in extranodal natural killer cell lymphoma (NKCL). Experimental Design: Promoter methylation was analyzed with global and locus-speci fic methylation assays in NKCL cases and NK cell lines. Gene expression profiles were used to identify genes for which aberrant promoter methylation was associated with transcriptional silencing. Selected DNA methylations were validated by RRBS, pyrosequencing, or q-MSP. Decitabine treatment was performed to evaluate reactivation of methylated genes. The tumor suppressor effect of silenced genes was evaluated functionally by reintroducing them into NK cell lines. Results: We observed significant promoter hypermethylation in most NKCL samples compared with normal NK cells. Correlation of global promoter methylation with gene expression profiles identi fied 95 genes with strong evidence for being silenced because of promoter methylation, including BCL2L11 (BIM), DAPK1, PTPN6 (SHP1), TET2, SOCS6, and ASNS. Known tumor suppressor genes were significantly overrepresented in this set of genes. Decitabine treatment of NK cell lines was associated with reexpression of all 10 selected methylated and silenced genes. Ectopic expression of frequently silenced BIM in two BIM-nonexpressing NK cell lines led to increased apoptosis and eventual elimination of BIM-transduced cells. It also sensitized these cell lines to chemotherapy-induced apoptosis. Similarly, reintroduction of SOCS6 significantly inhibited growth in SOCS6-nonexpressing NK cell lines. NK cell lines lacking ASNS expression showed increased sensitivity to treatment with L-asparaginase. Reintroduction of ASNS reduced drug sensitivity. Conclusion: Promoter region hypermethylation is frequent in NKCL, and aberrantly methylated genes are pathologically and clinically significant.

Original languageEnglish (US)
Pages (from-to)1699-1711
Number of pages13
JournalClinical Cancer Research
Volume21
Issue number7
DOIs
StatePublished - Apr 1 2015

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Tumor Suppressor Genes
Natural Killer Cells
Methylation
Lymphoma
Cell Line
decitabine
Genes
Transcriptome
Apoptosis
Asparaginase
DNA Methylation
Genetic Promoter Regions
Research Design
Therapeutics
Drug Therapy

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

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Global promoter methylation analysis reveals novel candidate tumor suppressor genes in natural killer cell lymphoma. / Küçük, Can; Hu, Xiaozhou; Jiang, Bei; Klinkebiel, David L; Geng, Huimin; Gong, Qiang; Bouska, Alyssa; Iqbal, Javeed; Gaulard, Philippe; McKeithan, Timothy W.; Chan, Wing C.

In: Clinical Cancer Research, Vol. 21, No. 7, 01.04.2015, p. 1699-1711.

Research output: Contribution to journalArticle

Küçük, Can ; Hu, Xiaozhou ; Jiang, Bei ; Klinkebiel, David L ; Geng, Huimin ; Gong, Qiang ; Bouska, Alyssa ; Iqbal, Javeed ; Gaulard, Philippe ; McKeithan, Timothy W. ; Chan, Wing C. / Global promoter methylation analysis reveals novel candidate tumor suppressor genes in natural killer cell lymphoma. In: Clinical Cancer Research. 2015 ; Vol. 21, No. 7. pp. 1699-1711.
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abstract = "Purpose: To identify tumor suppressor genes epigenetically silenced by promoter hypermethylation in extranodal natural killer cell lymphoma (NKCL). Experimental Design: Promoter methylation was analyzed with global and locus-speci fic methylation assays in NKCL cases and NK cell lines. Gene expression profiles were used to identify genes for which aberrant promoter methylation was associated with transcriptional silencing. Selected DNA methylations were validated by RRBS, pyrosequencing, or q-MSP. Decitabine treatment was performed to evaluate reactivation of methylated genes. The tumor suppressor effect of silenced genes was evaluated functionally by reintroducing them into NK cell lines. Results: We observed significant promoter hypermethylation in most NKCL samples compared with normal NK cells. Correlation of global promoter methylation with gene expression profiles identi fied 95 genes with strong evidence for being silenced because of promoter methylation, including BCL2L11 (BIM), DAPK1, PTPN6 (SHP1), TET2, SOCS6, and ASNS. Known tumor suppressor genes were significantly overrepresented in this set of genes. Decitabine treatment of NK cell lines was associated with reexpression of all 10 selected methylated and silenced genes. Ectopic expression of frequently silenced BIM in two BIM-nonexpressing NK cell lines led to increased apoptosis and eventual elimination of BIM-transduced cells. It also sensitized these cell lines to chemotherapy-induced apoptosis. Similarly, reintroduction of SOCS6 significantly inhibited growth in SOCS6-nonexpressing NK cell lines. NK cell lines lacking ASNS expression showed increased sensitivity to treatment with L-asparaginase. Reintroduction of ASNS reduced drug sensitivity. Conclusion: Promoter region hypermethylation is frequent in NKCL, and aberrantly methylated genes are pathologically and clinically significant.",
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T1 - Global promoter methylation analysis reveals novel candidate tumor suppressor genes in natural killer cell lymphoma

AU - Küçük, Can

AU - Hu, Xiaozhou

AU - Jiang, Bei

AU - Klinkebiel, David L

AU - Geng, Huimin

AU - Gong, Qiang

AU - Bouska, Alyssa

AU - Iqbal, Javeed

AU - Gaulard, Philippe

AU - McKeithan, Timothy W.

AU - Chan, Wing C.

PY - 2015/4/1

Y1 - 2015/4/1

N2 - Purpose: To identify tumor suppressor genes epigenetically silenced by promoter hypermethylation in extranodal natural killer cell lymphoma (NKCL). Experimental Design: Promoter methylation was analyzed with global and locus-speci fic methylation assays in NKCL cases and NK cell lines. Gene expression profiles were used to identify genes for which aberrant promoter methylation was associated with transcriptional silencing. Selected DNA methylations were validated by RRBS, pyrosequencing, or q-MSP. Decitabine treatment was performed to evaluate reactivation of methylated genes. The tumor suppressor effect of silenced genes was evaluated functionally by reintroducing them into NK cell lines. Results: We observed significant promoter hypermethylation in most NKCL samples compared with normal NK cells. Correlation of global promoter methylation with gene expression profiles identi fied 95 genes with strong evidence for being silenced because of promoter methylation, including BCL2L11 (BIM), DAPK1, PTPN6 (SHP1), TET2, SOCS6, and ASNS. Known tumor suppressor genes were significantly overrepresented in this set of genes. Decitabine treatment of NK cell lines was associated with reexpression of all 10 selected methylated and silenced genes. Ectopic expression of frequently silenced BIM in two BIM-nonexpressing NK cell lines led to increased apoptosis and eventual elimination of BIM-transduced cells. It also sensitized these cell lines to chemotherapy-induced apoptosis. Similarly, reintroduction of SOCS6 significantly inhibited growth in SOCS6-nonexpressing NK cell lines. NK cell lines lacking ASNS expression showed increased sensitivity to treatment with L-asparaginase. Reintroduction of ASNS reduced drug sensitivity. Conclusion: Promoter region hypermethylation is frequent in NKCL, and aberrantly methylated genes are pathologically and clinically significant.

AB - Purpose: To identify tumor suppressor genes epigenetically silenced by promoter hypermethylation in extranodal natural killer cell lymphoma (NKCL). Experimental Design: Promoter methylation was analyzed with global and locus-speci fic methylation assays in NKCL cases and NK cell lines. Gene expression profiles were used to identify genes for which aberrant promoter methylation was associated with transcriptional silencing. Selected DNA methylations were validated by RRBS, pyrosequencing, or q-MSP. Decitabine treatment was performed to evaluate reactivation of methylated genes. The tumor suppressor effect of silenced genes was evaluated functionally by reintroducing them into NK cell lines. Results: We observed significant promoter hypermethylation in most NKCL samples compared with normal NK cells. Correlation of global promoter methylation with gene expression profiles identi fied 95 genes with strong evidence for being silenced because of promoter methylation, including BCL2L11 (BIM), DAPK1, PTPN6 (SHP1), TET2, SOCS6, and ASNS. Known tumor suppressor genes were significantly overrepresented in this set of genes. Decitabine treatment of NK cell lines was associated with reexpression of all 10 selected methylated and silenced genes. Ectopic expression of frequently silenced BIM in two BIM-nonexpressing NK cell lines led to increased apoptosis and eventual elimination of BIM-transduced cells. It also sensitized these cell lines to chemotherapy-induced apoptosis. Similarly, reintroduction of SOCS6 significantly inhibited growth in SOCS6-nonexpressing NK cell lines. NK cell lines lacking ASNS expression showed increased sensitivity to treatment with L-asparaginase. Reintroduction of ASNS reduced drug sensitivity. Conclusion: Promoter region hypermethylation is frequent in NKCL, and aberrantly methylated genes are pathologically and clinically significant.

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